Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions DOI Creative Commons
Giuseppe Pezzotti, Eriko Ohgitani,

Yuki Fujita

et al.

ACS Infectious Diseases, Journal Year: 2023, Volume and Issue: 9(11), P. 2226 - 2251

Published: Oct. 18, 2023

The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream highly contagious and antibody-resistant strains, which in turn led to classifying as variant concern. We systematically collected Raman spectra from six subvariants available Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, BA.2.75) applied machine-learning algorithms decrypt their structural characteristics at molecular scale. Unique fingerprints sulfur-containing amino acid rotamers, purines pyrimidines, tyrosine phenol ring configurations, secondary protein structures clearly differentiated subvariants. These spectral characteristics, were linked infectiousness, transmissibility, propensity for immune evasion, revealed evolutionary motifs be compared with outputs studies. availability "metabolomic snapshot", was then translated into barcode enable prompt subvariant identification, opened way rationalize real-time activity variability. As proof concept, we procedure nasal swab sample retrieved patient identified its by coupling commercially magnetic bead technology our newly developed analyses.

Language: Английский

Impact of African-Specific ACE2 Polymorphisms on Omicron BA.4/5 RBD Binding and Allosteric Communication Within the ACE2–RBD Protein Complex DOI Open Access
Victor Barozi, Özlem Taştan Bishop

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(3), P. 1367 - 1367

Published: Feb. 6, 2025

Severe acute respiratory symptom coronavirus 2 (SARS-CoV-2) infection occurs via the attachment of spike (S) protein’s receptor binding domain (RBD) to human ACE2 (hACE2). Natural polymorphisms in hACE2, particularly at interface, may alter RBD–hACE2 interactions, potentially affecting viral infectivity across populations. This study identified effects six naturally occurring hACE2 with high allele frequency African population (S19P, K26R, M82I, K341R, N546D and D597Q) on interaction S protein RBD BA.4/5 Omicron sub-lineage through post-molecular dynamics (MD), inter-protein dynamic residue network (DRN) analyses. Inter-protein analysis suggested that K26R variation, highest aligns reports enhanced increased SARS-CoV-2 susceptibility. Conversely, S19P, showing fewest interactions largest distances, agrees studies indicating it hinders binding. The M82I substitution destabilized reducing contact from 92 (WT) 27. K341R variant, located distally, had allosteric contacts compared WThACE2. polymorphism has been linked affinity for Alpha, Beta Delta lineages. DRN analyses revealed networks, especially key residues involved enzyme activity Notably, S19P weaken hACE2–RBD while showed reduced centrality zinc chloride-coordinating residues, hinting impaired communication pathways. Overall, our findings show affect stability modulate influencing infectivity—key insights vaccine therapeutic development.

Language: Английский

Citations

1
Mutation N856K in spike reduces fusogenicity and infectivity of Omicron BA.1 DOI Creative Commons

Chunyun Sun,

Huiyu Wang, Ji Yang

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: Feb. 22, 2023

Language: Английский

Citations

15
Structural and Energetic Insights into SARS-CoV-2 Evolution: Analysis of hACE2–RBD Binding in Wild-Type, Delta, and Omicron Subvariants DOI Open Access

Can Tang,

Cecylia S. Lupala, Ding Wang

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(8), P. 3776 - 3776

Published: April 17, 2025

The evolution of SARS-CoV-2, particularly the emergence Omicron variants, has raised questions regarding changes in its binding affinity to human angiotensin-converting enzyme 2 receptor (hACE2). Understanding impact mutations on interaction between receptor-binding domain (RBD) spike protein and hACE2 is critical for evaluating viral transmissibility, immune evasion, efficacy therapeutic strategies. Here, we used molecular dynamics (MD) simulations energy calculations investigate structural energetic differences hACE2- RBD complexes wild-type (WT), Delta, subvariants. Our results indicate that Delta first variants showed highest second-highest among studied. Furthermore, while exhibit increased stability altered electrostatic potential at hACE2–RBD interface when compared ancestral WT, their strength does not consistently increase with evolution. Moreover, newer subvariants like JN.1 a bimodal conformational strategy, alternating high-affinity state low-affinity state, which could potentially facilitate evasion. These findings suggest that, addition enhanced affinity, other factors, such as evasion adaptability, shape SARS-CoV-2

Language: Английский

Citations

0
Computational analysis of the sequence-structure relation in SARS-CoV-2 spike protein using protein contact networks DOI Creative Commons
Pietro Hiram Guzzi, Luisa Di Paola, Barbara Puccio

et al.

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Feb. 17, 2023

Abstract The structure of proteins impacts directly on the function they perform. Mutations in primary sequence can provoke structural changes with consequent modification functional properties. SARS-CoV-2 have been extensively studied during pandemic. This wide dataset, related to and structure, has enabled joint sequence-structure analysis. In this work, we focus S (Spike) protein relations between mutations variations, order shed light stemming from position mutated amino acid residues three different strains. We propose use contact network (PCN) formalism to: (i) obtain a global metric space compare various molecular entities, (ii) give explanation observed phenotype, (iii) provide context dependent descriptors single mutations. PCNs used Alpha, Delta, Omicron variants, found that omicron unique mutational pattern leading consequences other non-random distribution centrality along chain allowed (and functional)

Language: Английский

Citations

10
Revealing SARS-CoV-2 Mpro Mutation Cold and Hot Spots: Dynamic Residue Network Analysis Meets Machine Learning DOI Creative Commons
Victor Barozi,

Shrestha Chakraborty,

S. Govender

et al.

Computational and Structural Biotechnology Journal, Journal Year: 2024, Volume and Issue: 23, P. 3800 - 3816

Published: Oct. 23, 2024

Language: Английский

Citations

2
Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions DOI Creative Commons
Giuseppe Pezzotti, Eriko Ohgitani,

Yuki Fujita

et al.

ACS Infectious Diseases, Journal Year: 2023, Volume and Issue: 9(11), P. 2226 - 2251

Published: Oct. 18, 2023

The latest RNA genomic mutation of SARS-CoV-2 virus, termed the Omicron variant, has generated a stream highly contagious and antibody-resistant strains, which in turn led to classifying as variant concern. We systematically collected Raman spectra from six subvariants available Japan (i.e., BA.1.18, BA.2, BA.4, BA.5, XE, BA.2.75) applied machine-learning algorithms decrypt their structural characteristics at molecular scale. Unique fingerprints sulfur-containing amino acid rotamers, purines pyrimidines, tyrosine phenol ring configurations, secondary protein structures clearly differentiated subvariants. These spectral characteristics, were linked infectiousness, transmissibility, propensity for immune evasion, revealed evolutionary motifs be compared with outputs studies. availability "metabolomic snapshot", was then translated into barcode enable prompt subvariant identification, opened way rationalize real-time activity variability. As proof concept, we procedure nasal swab sample retrieved patient identified its by coupling commercially magnetic bead technology our newly developed analyses.

Language: Английский

Citations

2